Inbreeding increases homozygosity, which affects fertility by increasing the frequency of harmful recessive alleles. Impaired fertility reduces profitability of dairy cattle production by decreasing the lifetime milk production of the cow and increasing the costs related to inseminations and veterinary treatments. Genetic diversity is known to vary across the genome, which is why detecting the regions with lower genetic diversity could indicate inbreeding depression. The objective of this study was to estimate the effect of increased homozygosity for number of inseminations required to successfully conceive (AIS) in the Finnish Ayrshire population using runs of homozygosity (ROH) and haplotype analysis. Genomic information from 13 712 Finnish Ayrshire females with fertility phenotypes was analysed. Genotypes were obtained with the Illumina BovineLD v.2 BeadChip low-density panel and imputed to 50K density. The phenotypic records were pre-adjusted for the most important fixed effects prior to the estimation of inbreeding depression. Regional ROH-based inbreeding coefficients (FROH) were used as covariates in the mixed model equation. First, the chromosomal FROH was determined as the number SNPs in ROHs divided by the total number of SNPs in the chromosome. Based on the analyses, a 10% increase in FROH on chromosome 2 or 18 was associated with 0.04 or 0.03 more inseminations for heifers, respectively (P-values < 0.01). Similarly, FROH estimated on chromosome 15 was associated with 0.05 more inseminations for the second parity cows (P-value < 0.01). Next, an intra-chromosomal sliding window approach was applied to locate more precisely the chromosomal regions showing inbreeding depression. Here FROH was calculated as the number of SNPs in ROHs belonging to the window divided by the total number of SNPs in the window. Regions associated with inbreeding depression on AIS were found near the beginning of chromosome 2 and towards the ends of chromosomes 15 and 18. The found regions were then examined for homozygous haplotypes associated with increased AIS. The analysis revealed common homozygous haplotypes that were associated with 0.09 or 0.10 more inseminations on chromosomes 2 and 18 for heifers, respectively. Similarly a common haplotype on chromosome 15 was associated with 0.15 more inseminations for second parity cows. Keywords: inbreeding, inbreeding depression, fertility, runs of homozygosity, haplotype
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Biology - Reproduction 2, , 423, 2018
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